Issues running Ciftify on fMRIPrep outputs

Is there a way I can get some support for fmriprep_ciftify_bids_app? I’ve tried to run it and it crashed

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Hi @urielias,

I’ve moderated your post to initiate a new issue, instead of continuing on an old (and probably unrelated) conversation.

Please, add more details in order to make it possible for us to help you. What did you try? What documentation are you following? What are the errors you get?


Thanks Esteban and sorry it took so long -
I’m not sure how to edit so I’ll write the details here.

my BIDS dir is: $BASE/Nifti/
so for instance I can type and get

$ ls -l $BASE/Nifti/sub-AlZi/ses-01/func/sub-AlZi_ses-01_task-rest_run-001_bold.nii.gz
-rwxrwxrwx 1 vr vr 43315233 Sep 12 07:25 /mnt/d/Repositories/Assuta/Nifti/sub-AlZi/ses-01/func/sub-AlZi_ses-01_task-rest_run-001_bold.nii.

Also, $BASE/Nifti contains freesurfer and fmriprep subdirs with the products of fMRIPrep - the results of

fmriprep-docker $BASE/Nifti $BASE participant --participant-label AlZi --fs-license-file /usr/local/freesurfer/license.txt --use-aroma

Now I type:

docker run -ti --rm -v $BASE/Nifti:/data:ro -v $BASE/ciftify:/out -v $BASE:/base -v $FS_LICENSE_DIR:/fs-license tigrlab/fmriprep_ciftify:latest /data /out participant --participant_label=AlZi --session_label=01 --fs-license /fs-license/license.txt --task_label=rest --read-from-derivatives /base

And get

No preprocessed derivative for bold <BIDSFile filename='sub-AlZi/ses-01/func/sub-AlZi_ses-01_task-rest_run-001_bold.nii.gz'> not found. Skipping ciftify_subject_fmri. Please check preprocessing pipeline for errors

It’s supposed to be pretty straightforward, but I don’t understand what is it that I’m doing wrong…

Thanks again